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  <title>Filter DNA</title>
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  <div class="category">
    Format Conversion
  </div>

  <div class="program">
    <a href="combine_fasta.html" onmouseover="self.status='Combines multiple FASTA entries into a single sequence.'; return true;" onmouseout="self.status=' '; return true;">-Combine FASTA</a><br />
    <a href="embl_fasta.html" onmouseover="self.status='Returns the entire sequence contained in an EMBL file in FASTA format.'; return true;" onmouseout="self.status=' '; return true;">-EMBL to FASTA</a><br />
    <a href="embl_feat.html" onmouseover="self.status='Parses the feature table of an EMBL file and returns the feature sequences.'; return true;" onmouseout="self.status=' '; return true;">-EMBL Feature Extractor</a><br />
    <a href="embl_trans.html" onmouseover="self.status='Parses the feature table of an EMBL file and returns the protein translations.'; return true;" onmouseout="self.status=' '; return true;">-EMBL Trans Extractor</a><br />
    <a href="filter_dna.html" onmouseover="self.status='Removes non-DNA characters from text.'; return true;" onmouseout="self.status=' '; return true;">-Filter DNA</a><br />
    <a href="filter_protein.html" onmouseover="self.status='Removes non-protein characters from text.'; return true;" onmouseout="self.status=' '; return true;">-Filter Protein</a><br />
    <a href="genbank_fasta.html" onmouseover="self.status='Returns the entire sequence contained in a GenBank file in FASTA format.'; return true;" onmouseout="self.status=' '; return true;">-GenBank to FASTA</a><br />
    <a href="genbank_feat.html" onmouseover="self.status='Parses the feature table of a GenBank file and returns the feature sequences.'; return true;" onmouseout="self.status=' '; return true;">-GenBank Feature Extractor</a><br />
    <a href="genbank_trans.html" onmouseover="self.status='Parses the feature table of a GenBank file and returns the protein translations.'; return true;" onmouseout="self.status=' '; return true;">-GenBank Trans Extractor</a><br />
    <a href="one_to_three.html" onmouseover="self.status='Converts single letter amino acid codes to three letter codes.'; return true;" onmouseout="self.status=' '; return true;">-One to Three</a><br />
    <a href="range_extract_dna.html" onmouseover="self.status='Reads a list of positions and ranges and returns those parts of a DNA sequence.'; return true;" onmouseout="self.status=' '; return true;">-Range Extractor DNA</a><br />
    <a href="range_extract_protein.html" onmouseover="self.status='Reads a list of positions and ranges and returns those parts of a protein sequence.'; return true;" onmouseout="self.status=' '; return true;">-Range Extractor Protein</a><br />
    <a href="rev_comp.html" onmouseover="self.status='Determines the reverse-complement, reverse, or complement of the sequence you enter.'; return true;" onmouseout="self.status=' '; return true;">-Reverse Complement</a><br />
    <a href="split_codons.html" onmouseover="self.status='Separates bases according to codon position.'; return true;" onmouseout="self.status=' '; return true;">-Split Codons</a><br />
    <a href="split_fasta.html" onmouseover="self.status='Converts a FASTA sequence into multiple sequences.'; return true;" onmouseout="self.status=' '; return true;">-Split FASTA</a><br />
    <a href="three_to_one.html" onmouseover="self.status='Converts three letter amino acid codes to one letter codes.'; return true;" onmouseout="self.status=' '; return true;">-Three to One</a><br />
    <a href="window_extract_dna.html" onmouseover="self.status='Returns DNA sequence segments specified by a position and window size.'; return true;" onmouseout="self.status=' '; return true;">-Window Extractor DNA</a><br />
    <a href="window_extract_protein.html" onmouseover="self.status='Returns protein sequence segments specified by a position and window size.'; return true;" onmouseout="self.status=' '; return true;">-Window Extractor Protein</a>
  </div>

  <div class="category">
    Sequence Analysis
  </div>

  <div class="program">
    <a href="codon_plot.html" onmouseover="self.status='Plots codon frequency (according to the codon table you enter) for each codon in a DNA sequence.'; return true;" onmouseout="self.status=' '; return true;">-Codon Plot</a><br />
    <a href="codon_usage.html" onmouseover="self.status='Returns a standard codon usage table.'; return true;" onmouseout="self.status=' '; return true;">-Codon Usage</a><br />
    <a href="cpg_islands.html" onmouseover="self.status='Returns a list of potential CpG islands.'; return true;" onmouseout="self.status=' '; return true;">-CpG Islands</a><br />
    <a href="dna_mw.html" onmouseover="self.status='Calculates the molecular weight of DNA sequences.'; return true;" onmouseout="self.status=' '; return true;">-DNA Molecular Weight</a><br />
    <a href="dna_pattern.html" onmouseover="self.status='Returns positions of the patterns you enter.'; return true;" onmouseout="self.status=' '; return true;">-DNA Pattern Find</a><br />
    <a href="dna_stats.html" onmouseover="self.status='Returns basic sequence statistics.'; return true;" onmouseout="self.status=' '; return true;">-DNA Stats</a><br />
    <a href="fuzzy_search_dna.html" onmouseover="self.status='Returns sequences that are identical or similar to a query sequence.'; return true;" onmouseout="self.status=' '; return true;">-Fuzzy Search DNA</a><br />
    <a href="fuzzy_search_protein.html" onmouseover="self.status='Returns sequences that are identical or similar to a query sequence.'; return true;" onmouseout="self.status=' '; return true;">-Fuzzy Search Protein</a><br />
    <a href="ident_sim.html" onmouseover="self.status='Accepts aligned sequences in FASTA format and calculates the identity and similarity of each sequence pair.'; return true;" onmouseout="self.status=' '; return true;">-Ident and Sim</a><br />
    <a href="multi_rev_trans.html" onmouseover="self.status='Can be used to predict a DNA sequence in another species using a protein sequence alignment.'; return true;" onmouseout="self.status=' '; return true;">-Multi Rev Trans</a><br />
    <a href="mutate_for_digest.html" onmouseover="self.status='Finds DNA sequences that can easily be converted to a restriction site.'; return true;" onmouseout="self.status=' '; return true;">-Mutate for Digest</a><br />
    <a href="orf_find.html" onmouseover="self.status='Determines the positions of open reading frames.'; return true;" onmouseout="self.status=' '; return true;">-ORF Finder</a><br />
    <a href="pairwise_align_codons.html" onmouseover="self.status='Returns the optimal global alignment for two coding DNA sequences.'; return true;" onmouseout="self.status=' '; return true;">-Pairwise Align Codons</a><br />
    <a href="pairwise_align_dna.html" onmouseover="self.status='Returns the optimal global alignment for two DNA sequences.'; return true;" onmouseout="self.status=' '; return true;">-Pairwise Align DNA</a><br />
    <a href="pairwise_align_protein.html" onmouseover="self.status='Returns the optimal global alignment for two protein sequences.'; return true;" onmouseout="self.status=' '; return true;">-Pairwise Align Protein</a><br />
    <a href="pcr_primer_stats.html" onmouseover="self.status='Returns a report describing PCR primer properties'; return true;" onmouseout="self.status=' '; return true;">-PCR Primer Stats</a><br />
    <a href="pcr_products.html" onmouseover="self.status='Generates PCR products from a template and two primer sequences.'; return true;" onmouseout="self.status=' '; return true;">-PCR Products</a><br />
    <a href="protein_gravy.html" onmouseover="self.status='Returns the grand average of hydropathy value of protein sequences.'; return true;" onmouseout="self.status=' '; return true;">-Protein GRAVY</a><br />
    <a href="protein_iep.html" onmouseover="self.status='Returns the predicted isoelectric point of protein sequences.'; return true;" onmouseout="self.status=' '; return true;">-Protein Isoelectric Point</a><br />
    <a href="protein_mw.html" onmouseover="self.status='Calculates the molecular weight of protein sequences.'; return true;" onmouseout="self.status=' '; return true;">-Protein Molecular Weight</a><br />
    <a href="protein_pattern.html" onmouseover="self.status='Returns positions of the patterns you enter.'; return true;" onmouseout="self.status=' '; return true;">-Protein Pattern Find</a><br />
    <a href="protein_stats.html" onmouseover="self.status='Returns basic sequence statistics.'; return true;" onmouseout="self.status=' '; return true;">-Protein Stats</a><br />
    <a href="rest_digest.html" onmouseover="self.status='Converts the sequence you enter into restriction fragments.'; return true;" onmouseout="self.status=' '; return true;">-Restriction Digest</a><br />
    <a href="rest_summary.html" onmouseover="self.status='Returns the number and positions of restriction sites.'; return true;" onmouseout="self.status=' '; return true;">-Restriction Summary</a><br />
    <a href="rev_trans.html" onmouseover="self.status='Can be used to convert protein into DNA.'; return true;" onmouseout="self.status=' '; return true;">-Reverse Translate</a><br />
    <a href="translate.html" onmouseover="self.status='Returns the translation in the reading frame you specify.'; return true;" onmouseout="self.status=' '; return true;">-Translate</a>
  </div>

  <div class="category">
    Sequence Figures
  </div>

  <div class="program">
    <a href="color_align_cons.html" onmouseover="self.status='Colors a sequence alignment based on sequence conservation.'; return true;" onmouseout="self.status=' '; return true;">-Color Align Conservation</a><br />
    <a href="color_align_prop.html" onmouseover="self.status='Colors a protein alignment based on biochemical properties of residues.'; return true;" onmouseout="self.status=' '; return true;">-Color Align Properties</a><br />
    <a href="group_dna.html" onmouseover="self.status='Numbers and groups DNA according to your specifications.'; return true;" onmouseout="self.status=' '; return true;">-Group DNA</a><br />
    <a href="group_protein.html" onmouseover="self.status='Numbers and groups amino acids according to your specifications.'; return true;" onmouseout="self.status=' '; return true;">-Group Protein</a><br />
    <a href="primer_map.html" onmouseover="self.status='Shows PCR primer annealing sites, translations, and restriction sites.'; return true;" onmouseout="self.status=' '; return true;">-Primer Map</a><br />
    <a href="rest_map.html" onmouseover="self.status='Shows restriction sites and protein translations.'; return true;" onmouseout="self.status=' '; return true;">-Restriction Map</a><br />
    <a href="trans_map.html" onmouseover="self.status='Shows protein translations.'; return true;" onmouseout="self.status=' '; return true;">-Translation Map</a>
  </div>

  <div class="category">
    Random Sequences
  </div>

  <div class="program">
    <a href="mutate_dna.html" onmouseover="self.status='Introduces random mutations into DNA sequences.'; return true;" onmouseout="self.status=' '; return true;">-Mutate DNA</a><br />
    <a href="mutate_protein.html" onmouseover="self.status='Introduces random mutations into protein sequences.'; return true;" onmouseout="self.status=' '; return true;">-Mutate Protein</a><br />
    <a href="random_coding_dna.html" onmouseover="self.status='Generates a random coding sequence of the length you specify.'; return true;" onmouseout="self.status=' '; return true;">-Random Coding DNA</a><br />
    <a href="random_dna.html" onmouseover="self.status='Generates a random DNA sequence of the length you specify.'; return true;" onmouseout="self.status=' '; return true;">-Random DNA Sequence</a><br />
    <a href="random_dna_regions.html" onmouseover="self.status='Replaces regions of the DNA sequences you enter with random bases.'; return true;" onmouseout="self.status=' '; return true;">-Random DNA Regions</a><br />
    <a href="random_protein.html" onmouseover="self.status='Generates a random protein sequence of the length you specify.'; return true;" onmouseout="self.status=' '; return true;">-Random Protein Sequence</a><br />
    <a href="random_protein_regions.html" onmouseover="self.status='Replaces regions of the protein sequences you enter with random residues.'; return true;" onmouseout="self.status=' '; return true;">-Random Protein Regions</a><br />
    <a href="sample_dna.html" onmouseover="self.status='Samples bases from a DNA sequence with replacement.'; return true;" onmouseout="self.status=' '; return true;">-Sample DNA</a><br />
    <a href="sample_protein.html" onmouseover="self.status='Samples residues from a protein sequence with replacement.'; return true;" onmouseout="self.status=' '; return true;">-Sample Protein</a><br />
    <a href="shuffle_dna.html" onmouseover="self.status='Randomly shuffles the DNA sequences you enter.'; return true;" onmouseout="self.status=' '; return true;">-Shuffle DNA</a><br />
    <a href="shuffle_protein.html" onmouseover="self.status='Randomly shuffles the protein sequences you enter.'; return true;" onmouseout="self.status=' '; return true;">-Shuffle Protein</a>
  </div>

  <div class="category">
    Miscellaneous
  </div>

  <div class="program">
    <a href="iupac.html" onmouseover="self.status='IUPAC codes for DNA and protein.'; return true;" onmouseout="self.status=' '; return true;">-IUPAC codes</a><br />
    <a href="genetic_code.html" onmouseover="self.status='The genetic codes used in the Sequence Manipulation Suite.'; return true;" onmouseout="self.status=' '; return true;">-Genetic codes</a><br />
    <a href="browser_compat.html" onmouseover="self.status='Browser compatibility.'; return true;" onmouseout="self.status=' '; return true;">-Browser compatibility</a><br />
    <a href="mirror.html" onmouseover="self.status='Mirror the Sequence Manipulation Suite.'; return true;" onmouseout="self.status=' '; return true;">-Mirror this site</a><br />
    <a href="mirror.html" onmouseover="self.status='Use the Sequence Manipulation Suite off-line.'; return true;" onmouseout="self.status=' '; return true;">-Use this site off-line</a><br />
    <a href="about.html" onmouseover="self.status='About the Sequence Manipulation Suite.'; return true;" onmouseout="self.status=' '; return true;">-About this site</a><br />
    <a href="acknowledgments.html" onmouseover="self.status='Acknowledgments.'; return true;" onmouseout="self.status=' '; return true;">-Acknowledgments</a><br />
    <a href="reference.html" onmouseover="self.status='Citing the Sequence Manipulation Suite.'; return true;" onmouseout="self.status=' '; return true;">-Reference</a>
  </div>
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            The Sequence Manipulation Suite Copyright &copy; 2000, 2004 Paul Stothard. Send questions and comments to stothard@ualberta.ca
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                <td class="sms">Sequence Manipulation Suite:</td>
              </tr>

              <tr>
                <td class="title">Filter DNA</td>
              </tr>

              <tr>
                <td class="description">
                  Filter DNA removes non-DNA characters from text. Use this program when you wish to remove digits and blank spaces from a sequence to make it suitable for other applications.<br />
                  <br />

                  <form action="" name="main_form" id="main_form">
                    Paste the text into the text area below. Input limit is 500000 characters.<br />
                    <textarea rows="6" cols="61">
      1 ttaagatttg cgctttgcca actgtacacc caacctcggt 
      41 ttattgtcga acctcccgct tgtgccgcca tctgcatata 
      81 gatcccggtc agtccgtcac attctgccaa ttgagtatcc 
     121 tcgaagtctt attccacgtg ctcaaagcaa gggtatcgta 
     161 cagtgataac cgcctcgtgc agatccaaat tctcgattaa 
     201 cactcaagta ctgattttta tcatcaggta actaaaaact 
     241 cacaatttga agcaccagcg agaatcgttc tattctctag 
     281 cttcgcaaca tcgacagttg taatggcata acttcggcat 
     321 tcatagtggc tgagtttagc ggactaagcg aaaaactggt 
     361 cgttagatct tcctcaccat gattttacaa gaaaggtgaa 
     401 ctcaatttga cggcggtaaa gttagatggc tacgcgcgac 
     441 aagtctccgt atcgtcatga aattagcgaa gaggtaatgg 
     481 caaagcttgg ctacgaatac aggagcgcgc tgtgattaca 
     521 gtagggttag gatagcgaaa acgttcaacg tggatagact 
     561 cttatcggca cacgatcata tgcttccaag gttcccaagg 
     601 cgaattacta gggtgcacag agctacgagt acgctgtccg 
     641 gcttgattcg ctcgtacatc cactgttcaa aaagctccga 
     681 taccgacgat cactctcgat ctctgtgtgg gacgcactta 
     721 ttgtggaatc agtcaaccag tgaagcattc acatgtacgt 
     761 ggtacggcac gccgtggtat gttagcgttc cctgcgccgc 
     801 aagtaaaccc ttcagctgtc acctcctata gtaacacgct 
     841 cgcatgcaga gcctagcacc ttagctctga gttgcctgcc 
     881 ggaaggatat attctgtatg tgattaaagc gaagtcaaag 
     921 taaacccccc acatgcagac ctgggtaaat tctcactcag 
     961 ttgaaacgta ggggccaata cgtgtgtcct tgatactact
</textarea><br />

                    <div class="warning">
                      Please check the <a href="browser_compat.html">browser compatibility</a> page before using this program.
                    </div><input type="button" value="Submit" name="main_submit" onclick="try{filterDna(document)} catch(e) {alert('The following error was encountered: ' + e);}" /> <input type="button" value="Clear" onclick="document.forms[0].elements[0].value = ' '" /> <input type="reset" value="Reset" />

                    <ul>
                      <li><select>
                        <option value="[^gatcnGATCN]" selected="selected">
                          remove non 'gatcn' characters
                        </option>

                        <option value="[^gatcryswkmbdhvnxGATCRYSWKMBDHVNX]">
                          remove non 'gatcryswkmbdhvnx' characters
                        </option>

                        <option value="[tT]">
                          remove 't'
                        </option>

                        <option value="[uU]">
                          remove 'u'
                        </option>

                        <option value="\s">
                          remove white space
                        </option>

                        <option value="\d">
                          remove digits
                        </option>

                        <option value="[\s\d]">
                          remove only digits and white space
                        </option>

                        <option value="[^a-z]">
                          remove everything except lowercase text
                        </option>

                        <option value="[^A-Z]">
                          remove everything except uppercase text
                        </option>
                      </select></li>

                      <li><select>
                        <option value="" selected="selected">
                          replace removed characters with nothing
                        </option>

                        <option value="n">
                          replace removed characters with 'n'
                        </option>

                        <option value="N">
                          replace removed characters with 'N'
                        </option>

                        <option value="t">
                          replace removed characters with 't'
                        </option>

                        <option value="T">
                          replace removed characters with 'T'
                        </option>

                        <option value="u">
                          replace removed characters with 'u'
                        </option>

                        <option value="U">
                          replace removed characters with 'U'
                        </option>

                        <option value="-">
                          replace removed characters with '-'
                        </option>

                        <option value="?">
                          replace removed characters with '?'
                        </option>

                        <option value="*">
                          replace removed characters with '*'
                        </option>
                      </select></li>

                      <li><select>
                        <option value="uppercase">
                          convert remaining characters to uppercase
                        </option>

                        <option value="lowercase">
                          convert remaining characters to lowercase
                        </option>

                        <option value="saveCase" selected="selected">
                          don't change the case of remaining characters
                        </option>
                      </select></li>
                    </ul>
                  </form>*This page requires JavaScript. See <a href="browser_compat.html">browser compatibility.</a><br />
                  *You can <a href="mirror.html">mirror this page</a> or <a href="mirror.html">use it off-line</a>.<br />
                  <br />

                  <center>
                    <a href="filter_dna.html" target="_blank">new window</a> | <a href="index.html">home</a> | <a href="reference.html">citation</a>
                  </center><span class="version">Tue Jun 15 14:20:12 2010</span>
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